chr1-52642888-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001042693.3(SHISAL2A):c.208G>A(p.Val70Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000539 in 1,613,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001042693.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SHISAL2A | NM_001042693.3 | c.208G>A | p.Val70Ile | missense_variant | 2/3 | ENST00000517870.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SHISAL2A | ENST00000517870.2 | c.208G>A | p.Val70Ile | missense_variant | 2/3 | 1 | NM_001042693.3 | P1 | |
SHISAL2A | ENST00000401050.7 | n.401G>A | non_coding_transcript_exon_variant | 3/6 | 1 | ||||
SHISAL2A | ENST00000424164.1 | n.109G>A | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
SHISAL2A | ENST00000440303.5 | n.358G>A | non_coding_transcript_exon_variant | 2/5 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152110Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000120 AC: 30AN: 249536Hom.: 0 AF XY: 0.000155 AC XY: 21AN XY: 135390
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461364Hom.: 0 Cov.: 31 AF XY: 0.0000784 AC XY: 57AN XY: 726996
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74418
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at